Patch up warmly this winter if you're running Java. That's the advice from .NET shop Microsoft, which reckons Oracle's platform is the single biggest target for hackers. Java proved the single most popular target in the 12-month period to the end of June, according to Microsoft's latest Security Intelligence Report has found here Running Java as a Web-browser Plugin is much more dangerous than Flash, and should disable the Java Applet Plugin.

Sorry, I wasn't clear enough.
I didn't said that java plugins are smart decision, they are awful. Flash is peace of shit also.
I just say that it's not Java/Oracle fault, just because from what I read there have update for issues and this is just cheap anti-advertising from MS. To blame platform because lazy developers and uneducated users is ridiculous.
That's really simple: vulnerability is found, now everybody knows about it, I begin to exploit vulnerability, updates are produce, nobody use them, I still exploit vulnerability.

MS allow outdated and cracked software on Windows. That made it the most popular "General purpose OS for masses on desktop and laptops". But everything has good and bad side, article is about bad side.

Actually I read only article not PDF, but when browse PDF I was shocked. Page 63 from 168 show a graphic where you could learn that detected Operating Systems exploits was doubled at the end of 2Q2011 and at second place after Java exploits. May be for 3Q2011 we should expect OS exploits to be more than Java.

It called backwards compatibility ... very important for businesses. TBH if a piece of software works why change it?

I and most people I know at least patch security updates on our systems. I'm not sure about Java, but for last 4 years I patched hundreds Oracle DB servers, Red Hat, OEL and HP-UX machines with security and bug fixing patches and they still works.
Most of the companies also pay for software support. For example Quest Software never broke Toad for Oracle for me, but produce some bug fixes, same with Altova. (That's closed software companies, with Open source is even easier.)
Masses are just ignorant and stupid. They care about their cars tires and fuel, to change oil, breaks , but never care about theirs computers systems, personal information, etcetera, etcetera.